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三种马卡罗尼西亚特有植物物种的转录组测序及简单序列重复标记开发

Transcriptome sequencing and simple sequence repeat marker development for three Macaronesian endemic plant species.

作者信息

White Oliver W, Doo Bethany, Carine Mark A, Chapman Mark A

机构信息

Plants Division, Natural History Museum, London SW7 5BD, United Kingdom; Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom.

Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom.

出版信息

Appl Plant Sci. 2016 Aug 23;4(8). doi: 10.3732/apps.1600050. eCollection 2016 Aug.

DOI:10.3732/apps.1600050
PMID:27610280
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5001862/
Abstract

PREMISE OF THE STUDY

Oceanic islands offer unparalleled opportunities to investigate evolutionary processes such as adaptation and speciation. However, few genomic resources are available for oceanic island endemics. In this study, we publish transcriptome sequences from three Macaronesian endemic plant species (Argyranthemum broussonetii [Asteraceae], Descurainia bourgaeana [Brassicaceae], and Echium wildpretii [Boraginaceae]) that are representative of lineages that have radiated in the region. In addition, the utility of transcriptome data for marker development is demonstrated.

METHODS AND RESULTS

Transcriptomes from the three plant species were sequenced, assembled, and annotated. Between 1972 and 2282 simple sequence repeats (SSRs) were identified for each taxon. Primers were designed and tested for 30 of the candidate SSRs identified in Argyranthemum, of which 12 amplified well across three species and eight were polymorphic.

CONCLUSIONS

We demonstrate here that a single transcriptome sequence is sufficient to identify hundreds of polymorphic SSR markers. The SSRs are applicable to a wide range of questions relating to the evolution of island lineages.

摘要

研究前提

海洋岛屿为研究适应和物种形成等进化过程提供了无与伦比的机会。然而，针对海洋岛屿特有物种的基因组资源却很少。在本研究中，我们公布了三种马卡罗尼西亚特有植物物种（茼蒿菊[菊科]、布尔盖亚麻荠[十字花科]和特内里费岛蓝蓟[紫草科]）的转录组序列，这些物种代表了在该地区辐射演化的谱系。此外，还展示了转录组数据在标记开发中的实用性。

方法与结果

对这三种植物物种的转录组进行了测序、组装和注释。每个分类单元鉴定出1972至2282个简单序列重复序列（SSRs）。针对茼蒿菊中鉴定出的30个候选SSRs设计并测试了引物，其中12个在三个物种中扩增良好，8个具有多态性。

结论

我们在此证明，单个转录组序列足以鉴定数百个多态性SSR标记。这些SSRs适用于与岛屿谱系进化相关的广泛问题。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5312/5001862/319a28ebd7a1/apps.1600050fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5312/5001862/a678816ee849/apps.1600050fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5312/5001862/18dad5aa7fb6/apps.1600050fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5312/5001862/cd5ad751600e/apps.1600050fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5312/5001862/319a28ebd7a1/apps.1600050fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5312/5001862/a678816ee849/apps.1600050fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5312/5001862/18dad5aa7fb6/apps.1600050fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5312/5001862/cd5ad751600e/apps.1600050fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5312/5001862/319a28ebd7a1/apps.1600050fig4.jpg

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